Re: [AMBER] problem with addIons in tleap

From: Wei Chen <cwbluesky.gmail.com>
Date: Fri, 22 Jul 2011 11:33:51 -0700

Hi, Dan,

I used AmberTools 1.2 / tleap to generate this some time ago. But also
tried using 1.5 recently. It behaved the same. The topology file is
too big to send by email (this is a big system). Instead, I attached a
figure to show what is going on. Red dots are waters. Cyan and blue
balls are ions.

The input for tleap as follows:

source leaprc.ff03
source leaprc.GLYCAM_06
X = loadpdb 3ije_mod.pdb
solvateBox X TIP3PBOX 15
addIons X Na+ 241 Cl- 203
charge X
savePdb X 3ije_wb.ff03.pdb
saveamberparm X 3ije_wb.ff03.prmtop 3ije_wb.ff03.prmcrd
quit


Thank you!

Wei


> On Fri, Jul 22, 2011 at 4:19 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>> Hi,
>>
>> This does seem like strange behavior. Can you provide some more
>> information so we can figure out what might be going on? What version
>> of AmberTools were you using (1.5?), what bugfixes are applied, which
>> program did you use (tleap, sleap, or xleap), and what input did you
>> give it? Also, could you attach the coords/topology that leap
>> generated? Thanks!
>>
>> -Dan
>>
>> On Fri, Jul 22, 2011 at 1:22 AM, Wei Chen <cwbluesky.gmail.com> wrote:
>>> Hi, All,
>>>
>>> After I solvated my protein, I used "addIons" to add ions to the
>>> system to reach certain ion concentration. I found that some ions were
>>> placed outside of the water box. Is this normal? When I used AMBER8
>>> long time ago, this did not happen. I was wondering if this is
>>> something with the new version of AmberTools.
>>>
>>> Thanks!
>>>
>>> Wei Chen
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>> _______________________________________________
>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>


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Received on Fri Jul 22 2011 - 12:00:02 PDT
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